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bobeobibo / phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages
MIT License
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Cannot download fasta sequences #6

Closed tauqeer9 closed 3 years ago

tauqeer9 commented 5 years ago

Hi This is a great tool, all steps work fine. However, I am not able to download the prophage sequences in fasta-format. The double-stranded DNA icon for BLAST works perfectly alright. But, the vertical arrow to download fasta sequences does not seem to work. In short, how can I extract fasta sequences of these prophage regions? Thanks.

PollyTikhonova commented 5 years ago

Hello, unfortunately, the server with the necessary script is down. But now the problem is fixed and the new version of phigaro is available now. Also, you can change the line at header of your html file: from <script src="https://fastcdn.org/FileSaver.js/1.1.20151003/FileSaver.min.js"></script> to <script src="https://cdn.jsdelivr.net/gh/bobeobibo/phigaro/scripts/FileSaver.min.js"></script>

tauqeer9 commented 5 years ago

Thanks. It works fine now. However, it would be nice to save prophage sequences of each sample in the result folder automatically, along with phg and html files (prefix with sample name). For few samples it is easy to download these fasta files manually, but will be difficult if there are large number of samples to analyze. Just a thought.

PollyTikhonova commented 5 years ago

At the bottom of the html page you can find two icons: to blast all and to download all

tauqeer9 commented 5 years ago

I am using this one-liner to generate phg and html files for 3 samples (In future, I plan to run on ~500 samples). Then, I open 3 html files to download their prophage fasta by clicking the download icon at the bottom corner, which is great. Is it possible to add fasta download/generate feature with -e option? So it produce ".phg", ".html" and ".fasta" for each sample (accession number in this example), instead of downloading them manually from the html file. I think PHASTER tool produces fasta format sequence for each sample.

###############

!/bin/bash

files=('CP016072' 'CP016073' 'CP032682' ) for file in "${files[@]}"; do phigaro -f FASTA/${file}.fasta -o RESULT/${file}.phg -p --not-open -c config.yml -t 16 -e txt html done #############

Thank you so much.

PollyTikhonova commented 5 years ago

Hello! We've added the feature you asked about! Try it in a new Phigaro 0.2.1.7 =)

tauqeer9 commented 5 years ago

Thank you so much. The newly added -s option downloads all the prophages in fasta format. It becomes easier to cluster all predicted prophages now. Thanks again for this great tool.

tauqeer9 commented 3 years ago

Hello I just updated to phigaro 2.2.6 using conda, and see that -s option to automatically download prophages in fasta format is no longer available. It would be nice to have this option for comparing all prophages. It is difficult to download them from the icon in the html file. Also, I can not find --wtp option with phigaro -h.

PollyTikhonova commented 3 years ago

Hello, sorry, I'll check tomorrow when and why I lost the -s option and restore it! About --wtp, it is a service option for WhatThePhage tool, so, it is not supposed for general usage